tbuckley/cabot-search huggingface dataset:
Taking Stock After Another Negative Erythropoietin Neuroprotection Trial
Authors: Thomas R. Wood, Sandra E. Juul
Journal: JAMA Network Open (2022)

Sven Wellmann, MD; Cornelia F. Hagmann, MD, PhD; Stefanie von Felten, PhD; Leonard Held, PhD; Katrin Klebermass-Schrehof, MD; Anita C. Truttmann, MD, PhD; Claudia Knöpfli, MSc; Jean-Claude Fauchère, MD, PhD; Christoph Bührer, MD; Hans Ulrich Bucher, MD, PhD; Christoph M. Rüegger, MD; Erythropoietin for the Repair of Cerebral Injury in Very Preterm Infants (EpoRepair) Investigators; Philipp Meyer; Gabriel Konetzny; Corinne Däster; Sven M Schulzke; Severin Kasser; Roland Gerull; Mathias Nelle; Benedikt Bubl; Walter Bär; Brigitte Scharrer; Thomas Riedel; Jean-François Tolsa; Bjarte Rogdo; Irene Hoigne; André Birkenmaier; Giancarlo Natalucci; Angelika Berger; Alexandra Thajer
Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies
Authors: Pradeepa Pushparaj, Andrea Nicoletto, Daniel J. Sheward, Hrishikesh Das, Xaquin Castro Dopico, Laura Perez Vidakovics, Leo Hanke, Mark Chernyshev, Sanjana Narang, Sungyong Kim, Julian Fischbach, Simon Ekström, Gerald McInerney, B. Martin Hällberg, Ben Murrell, Martin Corcoran, Gunilla B. Karlsson Hedestam
Journal: Immunity (2022)

The human immunoglobulin heavy-chain (IGH) locus is exceptionally polymorphic, with high levels of allelic and structural variation. Thus, germline IGH genotypes are personal, which may influence responses to infection and vaccination. For an improved understanding of inter-individual differences in antibody responses, we isolated SARS-CoV-2 spike-specific monoclonal antibodies from convalescent health care workers, focusing on the IGHV1-69 gene, which has the highest level of allelic variation of all IGHV genes. The IGHV1-69
Hydrogen-bond-driven self-assembly of chemiluminophore affording long-lasting in vivo imaging
Authors: Shuai Xu, Wenjing Pan, Lanlan Chen, Sulai Liu, Tian-Bing Ren, Hong-Wen Liu, Yongchao Liu, Shuang-Yan Huan, Lin Yuan, Xiao-Bing Zhang
Journal: Biomaterials (2022)
Placental Inflammation Leads to Abnormal Embryonic Heart Development
Authors: Eleanor J. Ward, Serena Bert, Silvia Fanti, Kerri M. Malone, Robert T. Maughan, Christina Gkantsinikoudi, Fabrice Prin, Lia Karina Volpato, Anna Paula Piovezan, Gerard J. Graham, Neil P. Dufton, Mauro Perretti, Federica M. Marelli-Berg, Suchita Nadkarni
Journal: Circulation (2022)

Placental heart development and embryonic heart development occur in parallel, and these organs have been proposed to exert reciprocal regulation during gestation. Poor placentation has been associated with congenital heart disease, an important cause of infant mortality. However, the mechanisms by which altered placental development can lead to congenital heart disease remain unresolved.
iHypoxia: An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals
Authors: Ze-Xian Liu, Panqin Wang, Qingfeng Zhang, Shihua Li, Yuxin Zhang, Yutong Guo, Chongchong Jia, Tian Shao, Lin Li, Han Cheng, Zhenlong Wang
Journal: Genomics Proteomics & Bioinformatics (2022)

Mammals have evolved mechanisms to sense hypoxia and induce hypoxic responses. Recently, high-throughput techniques have greatly promoted global studies of protein expression changes during hypoxia and the identification of candidate genes associated with hypoxia-adaptive evolution, which have contributed to the understanding of the complex regulatory networks of hypoxia. In this study, we developed an integrated resource for the expression dynamics of proteins in response to hypoxia (iHypoxia), and this database contains 2589 expression events of 1944 proteins identified by low-throughput experiments (LTEs) and 422,553 quantitative expression events of 33,559 proteins identified by high-throughput experiments from five mammals that exhibit a response to hypoxia. Various experimental details, such as the hypoxic experimental conditions, expression patterns, and sample types, were carefully collected and integrated. Furthermore, 8788 candidate genes from diverse species inhabiting low-oxygen environments were also integrated. In addition, we conducted an orthologous search and computationally identified 394,141 proteins that may respond to hypoxia among 48 animals. An enrichment analysis of human proteins identified from LTEs shows that these proteins are enriched in certain drug targets and cancer genes. Annotation of known posttranslational modification (PTM) sites in the proteins identified by LTEs reveals that these proteins undergo extensive PTMs, particularly phosphorylation, ubiquitination, and acetylation. iHypoxia provides a convenient and user-friendly method for users to obtain hypoxia-related information of interest. We anticipate that iHypoxia, which is freely accessible at https://ihypoxia.omicsbio.info, will advance the understanding of hypoxia and serve as a valuable data resource.
Immunogenicity of COVID-19 vaccines in solid organ transplant recipients: a systematic review and meta-analysis
Authors: Xinpei Chen, De Luo, Bingjie Mei, Juan Du, Xiangdong Liu, Hui Xie, Lin Liu, Song Su, Gang Mai
Journal: Clinical Microbiology and Infection (2022)

BackgroundSolid organ transplant (SOT) recipients are at increased risks of morbidity and mortality associated with COVID-19.ObjectivesThis study aimed to evaluate the immunogenicity of COVID-19 vaccines in SOT recipients.Data sourcesElectronic databases were searched for eligible reports published from 1 December 2019 to 31 May 2022.Study eligibility criteriaWe included reports evaluating the humoral immune response (HIR) or cellular immune response rate in SOT recipients after the administration of COVID-19 vaccines.ParticipantsSOT recipients who received COVID-19 vaccines.Assessment of risk of biasWe used the Newcastle-Ottawa scale to assess bias in case-control and cohort studies. For randomised-controlled trials, the Jadad Scale was used.MethodsWe used a random-effects model to calculate the pooled rates of immune response with 95% CI. We used a risk ratio (RR) with 95% CI for a comparison of immune responses between SOT and healthy controls.ResultsA total of 91 reports involving 11 886 transplant recipients (lung: 655; heart: 539; liver: 1946; and kidney: 8746) and 2125 healthy controls revealed pooled HIR rates after the 1st, 2nd, and 3rd COVID-19 vaccine doses in SOT recipients were 9.5% (95% CI, 7–11.9%), 43.6% (95% CI, 39.3–47.8%) and 55.1% (95% CI, 44.7–65.6%), respectively. For specific organs, the HIR rates were still low after 1st vaccine dose (lung: 4.4%; kidney: 9.4%; heart: 13.2%; liver: 29.5%) and 2nd vaccine dose (lung: 28.4%; kidney: 37.6%; heart: 50.3%; liver: 64.5%).ConclusionsA booster vaccination enhances the immunogenicity of COVID-19 vaccines in SOT; however, a significant share of the recipients still has not built a detectable HIR after receiving the 3rd dose. This finding calls for alternative approaches, including the use of monoclonal antibodies. In addition, lung transplant recipients need urgent booster vaccination to improve the immune response.
Reduced immunogenicity of BNT162b2 booster vaccination in combination with a tetravalent influenza vaccination: results of a prospective cohort study in 838 health workers
Authors: Helga Radner, Daniela Sieghart, Anselm Jorda, Clemens Fedrizzi, Timothy Hasenöhrl, Andrej Zdravkovic, Monika Redlberger-Fritz, Elisabeth Puchammer-Stoeckl, Karolina Anderle, Felix Bergmann, Christa Firbas, Galateja Jordakieva, Barbara Wagner, Helmuth Haslacher, Thomas Perkmann, Leonhard X Heinz, Michael Bonelli, Richard Crevenna, Daniel Aletaha, Markus Zeitlinger
Journal: Clinical Microbiology and Infection (2022)

ObjectiveTo investigate the immunogenicity and safety of BNT162b2 booster vaccination with and without a tetravalent influenza vaccine.MethodsA prospective, open-label cohort study on immunogenicity and safety of COVID-19 booster vaccination with or without a tetravalent influenza vaccine was performed. Eight hundred thirty-eight health care workers were included in the following study arms: BNT162b2 booster-only, influenza-vaccine-only or combination of both. Levels of antibodies against SARS-CoV-2 spike receptor binding domain, and haemagglutinin inhibition tested for four different influenza strains (A(H1N1)pdm09, A(H3N2), B/Victoria, B/Yamagata) were measured at the time of vaccination and 4 weeks later.ResultsAfter 4 weeks, median (interquartile range) levels of antibodies against the receptor binding domain of the viral spike (S) protein and relative change from baseline were high in individuals who received BNTb162b2 booster vaccination only (absolute: 16 600 [10 980–24 360] vs. 12 630 [8198–18 750] BAU/mL [p < 0.0001]; relative increase: 49% [23.6–95.3] vs. 40% [21.9–80.6] [p 0.048]; booster-only n = 521 vs. combination-arm n = 229 respectively). Results were confirmed after matching for sex, age, body mass index, baseline antibody levels and vaccine compound received for primary immunization (absolute: 13 930 [10 610–22 760] vs. 12 520 [8710–17 940]; [p 0.031]; relative increase: 55.7% [27.8–98.5] vs. 42.2% [22.9–74.5]; p 0.045). Adverse events were almost identical in the booster-only and the combination-arm, but numerically low in the influenza arm (525/536 [97.9%] vs. 235/240 [97.9%] vs. 26/33 [78.8 %]).DiscussionAlthough no safety concerns occurred, our study provides evidence on reduced immunogenicity of a BNT162b2 booster vaccination in combination with a tetravalent influenza vaccine. Further studies investigating new influenza variants as well as potential differences vaccine effectiveness are needed.
Clostridioides difficile infection with isolates of cryptic clade C-II: a genomic analysis of polymerase chain reaction ribotype 151
Authors: Quinten R. Ducarmon, Tjomme van der Bruggen, Céline Harmanus, Ingrid M.J.G. Sanders, Laura G.M. Daenen, Ad C. Fluit, Rolf H.A.M. Vossen, Susan L. Kloet, Ed J. Kuijper, Wiep Klaas Smits
Journal: Clinical Microbiology and Infection (2022)

ObjectivesWe report a patient case of pseudomembranous colitis associated with a monotoxin-producing Clostridioides difficile belonging to the very rarely diagnosed polymerase chain reaction (PCR) ribotype (RT) 151. To understand why this isolate was not identified using a routine commercial test, we performed a genomic analysis of RT151.MethodsIllumina short-read sequencing was performed on n = 11 RT151s from various geographical regions to study their genomic characteristics and relatedness. Subsequently, we used PacBio circular consensus sequencing to determine the complete genome sequence of isolates belonging to cryptic clades C–I and C-II, which includes the patient isolate.ResultsWe found that 1) RT151s are polyphyletic with isolates falling into clades 1 and cryptic clades C–I and C-II; 2) RT151 contains both nontoxigenic and toxigenic isolates and 3) RT151 C-II isolates contained monotoxin pathogenicity loci. The isolate from our patient case report contains a novel-pathogenicity loci insertion site, lacked tcdA and had a divergent tcdB sequence that might explain the failure of the diagnostic test.DiscussionThis study shows that RT151 encompasses both typical and cryptic clades and provides conclusive evidence for C. difficile infection due to clade C-II isolates that was hitherto lacking. Vigilance towards C. difficile infection as a result of cryptic clade isolates is warranted.
Plasma Progastrin-Releasing Peptide and Chromogranin A Assays for Diagnosing and Monitoring Lung Well-Differentiated Neuroendocrine Tumors: A Brief Report
Authors: Benjamin Nisman, Kira Oleinikov, Hovav Nechushtan, Ofra Maimon, Karine Atlan, Nir Peled, David Gross, Tamar Peretz, Amichay Meirovitz, Simona Grozinsky-Glasberg
Journal: Journal of Thoracic Oncology (2022)
TLR7 agonist RO7020531 versus placebo in healthy volunteers and patients with chronic hepatitis B virus infection: a randomised, observer-blind, placebo-controlled, phase 1 trial
Authors: Man-Fung Yuen, Rozalina Balabanska, Emmanuelle Cottreel, Ethan Chen, Dan Duan, Qiudi Jiang, Avinash Patil, Miriam Triyatni, Ruchi Upmanyu, Yonghong Zhu, Filippo Canducci, Edward J Gane
Journal: The Lancet Infectious Diseases (2022)
Melanomas in children and adolescents: Clinicopathologic features and survival outcomes
Authors: Mary-Ann El Sharouni, Robert V. Rawson, Alison J. Potter, Elizabeth C. Paver, James S. Wilmott, Arjen J. Witkamp, Vigfús Sigurdsson, Paul J. van Diest, Richard A. Scolyer, John F. Thompson, Serigne N. Lo, Carla H. van Gils
Journal: Journal of the American Academy of Dermatology (2022)
Longitudinal age differences in humoral responses to the COVID-19 vaccine in the elderly are lost after the third dose
Authors: María Del Mar Pozo-Balado, Ángel Bulnes-Ramos, Vanesa Garrido-Rodríguez, Israel Olivas-Martínez, Carmen Lozano, María Francisca González-Escribano, Manuel Leal, Yolanda M Pacheco
Journal: Journal of Infection (2022)
Mpox screening in high-risk populations finds no asymptomatic cases
Authors: Christophe Van Dijck, Irith De Baetselier, Chris Kenyon, Laurens Liesenborghs, Koen Vercauteren, Marjan Van Esbroeck, Christophe Van Dijck, Irith De Baetselier, Chris Kenyon, Isabel Brosius, Laurens Liesenborghs, Dorien Van den Bossche, Eric Florence, Johan van Griensven, Emmanuel Bottieau, Patrick Soentjens, Nicole Berens-Riha, Thibaut Vanbaelen, Maartje Van Frankenhuijsen, Marc Vandenbruaene, Veerle Huyst, Kristien Wouters, Ludwig Apers, Ilse Kint, Séverine Caluwaerts, Jasmine Coppens, Marjan Van Esbroeck, Koen Vercauteren
Journal: The Lancet Microbe (2022)
Endoscopic surveillance with systematic random biopsy for the early diagnosis of hereditary diffuse gastric cancer: a prospective 16-year longitudinal cohort study
Authors: Colin Y C Lee, Adriaan Olivier, Judith Honing, Anne-Marie Lydon, Susan Richardson, Maria O'Donovan, Marc Tischkowitz, Rebecca C Fitzgerald, Massimiliano di Pietro
Journal: The Lancet Oncology (2022)

Hereditary diffuse gastric cancer, generally caused by germline pathogenic variants in CDH1, presents with early-onset signet ring cell carcinoma. Prophylactic total gastrectomy is the definitive treatment. Endoscopic surveillance can inform the timing of prophylactic total gastrectomy through detection of microscopic signet ring cell carcinoma foci. However, evidence is scarce about the optimal endoscopic sampling technique and characterisation of signet ring cell carcinoma foci in hereditary diffuse gastric cancer. We aimed to formally assess the diagnostic yield of different sampling strategies and to identify criteria for the characterisation of endoscopic lesions.For this prospective longitudinal cohort study, we included individuals aged 18 years or older at the Cambridge University Hospitals National Health Service (NHS) Foundation Trust who fulfilled testing criteria for hereditary diffuse gastric cancer between June 1, 2005, and July 31, 2021. The primary outcome was detection of intramucosal signet ring cell carcinoma foci. We assessed the detection rate and anatomical location of signet ring cell carcinoma in random biopsy samples taken according to a systematic protocol compared with biopsies targeted to endoscopic findings. Endoscopic lesions were examined with white-light and narrow band imaging with magnification to assess the likelihood of cancerous foci.145 individuals were included, of whom 68 (47%) were male and 92 (63%) carried the CDH1 pathogenic variant. 58 (40%) patients were diagnosed with invasive signet ring cell carcinoma over a median follow-up time of 51 months (IQR 18-80). The first diagnosis of signet ring cell carcinoma was most commonly made from random biopsies (29 [50%] of 58 patients), rather than targeted biopsies (15 [26%] patients). The anatomical distribution of signet ring cell carcinoma foci detected by random biopsies more accurately reflected those identified in prophylactic total gastrectomy specimens than did targeted biopsies. Omitting random biopsies in our cohort would have led to an under-diagnosis rate of 42%. Using a novel panel of endoscopic criteria, gastric lesions containing signet ring cell carcinoma were predicted with a sensitivity of 67·3% and a specificity of 90·2%.Random biopsies enhance the early detection of signet ring cell carcinoma and are complementary to targeted biopsies in surveillance of hereditary diffuse gastric cancer. This sampling method should be the standard of care when performing all surveillance endoscopies for individuals with hereditary diffuse gastric cancer.UK Medical Research Council.
Single‐cell transcriptomics reveals distinct cell response between acute and chronic pulmonary infection of <i>Pseudomonas aeruginosa</i>
Authors: Xueli Hu, Mingbo Wu, Teng Ma, Yige Zhang, Chaoyu Zou, Ruihuan Wang, Yongxin Zhang, Yuan Ren, Qianqian Li, Huan Liu, Heyue Li, Taolin Wang, Xiaolong Sun, Yang Yang, Miao Tang, Xuefeng Li, Jing Li, Xiang Gao, Taiwen Li, Xikun Zhou
Journal: MedComm (2022)

Knowledge of the changes in the immune microenvironment during pulmonary bacterial acute and chronic infections is limited. The dissection of immune system may provide a basis for effective therapeutic strategies against bacterial infection. Here, we describe a single immune cell atlas of mouse lungs after acute and chronic
Prevalence of post-traumatic stress disorder and common mental disorders in health-care workers in England during the COVID-19 pandemic: a two-phase cross-sectional study
Authors: Hannah R Scott, Sharon A M Stevelink, Rafael Gafoor, Danielle Lamb, Ewan Carr, Ioannis Bakolis, Rupa Bhundia, Mary Jane Docherty, Sarah Dorrington, Sam Gnanapragasam, Siobhan Hegarty, Matthew Hotopf, Ira Madan, Sally McManus, Paul Moran, Emilia Souliou, Rosalind Raine, Reza Razavi, Danny Weston, Neil Greenberg, Simon Wessely
Journal: The Lancet Psychiatry (2022)
Associations between psychological intervention for anxiety disorders and risk of dementia: a prospective cohort study using national health-care records data in England
Authors: Josh Stott, Rob Saunders, Roopal Desai, Georgia Bell, Caroline Fearn, Joshua E J Buckman, Barbara Brown, Shirley Nurock, Stewart Michael, Paul Ware, Natalie L Marchant, Elisa Aguirre, Miguel Rio, Claudia Cooper, Stephen Pilling, Marcus Richards, Amber John
Journal: The Lancet Healthy Longevity (2022)

Meta-analyses support an association between anxiety in older adulthood and dementia. The aim of this study was to use routinely collected health data to test whether treatment of anxiety disorders through psychological intervention is associated with a lower incidence of dementia.
Long COVID: The latest manifestations, mechanisms, and potential therapeutic interventions
Authors: Shi‐ting He, Kexin Wu, Zixuan Cheng, Mengjie He, Ruolan Hu, Ning Fan, Lin Shen, Qirui Li, Huahao Fan, Yigang Tong
Journal: MedComm (2022)

COVID-19 caused by SARS-CoV-2 infection affects humans not only during the acute phase of the infection, but also several weeks to 2 years after the recovery. SARS-CoV-2 infects a variety of cells in the human body, including lung cells, intestinal cells, vascular endothelial cells, olfactory epithelial cells, etc. The damages caused by the infections of these cells and enduring immune response are the basis of long COVID. Notably, the changes in gene expression caused by viral infection can also indirectly contribute to long COVID. We summarized the occurrences of both common and uncommon long COVID, including damages to lung and respiratory system, olfactory and taste deficiency, damages to myocardial, renal, muscle, and enduring inflammation. Moreover, we provided potential treatments for long COVID symptoms manifested in different organs and systems, which were based on the pathogenesis and the associations between symptoms in different organs. Importantly, we compared the differences in symptoms and frequency of long COVID caused by breakthrough infection after vaccination and infection with different variants of concern, in order to provide a comprehensive understanding of the characteristics of long COVID and propose improvement for tackling COVID-19.
Management of Acute Coronary Syndrome in the Older Adult Population: A Scientific Statement From the American Heart Association
Authors: Abdulla A. Damluji, Daniel E. Forman, Tracy Y. Wang, Joanna Chikwe, Vijay Kunadian, Michael W. Rich, Bessie A. Young, Robert L. Page, Holli A. DeVon, Karen P. Alexander
Journal: Circulation (2022)

Diagnostic and therapeutic advances during the past decades have substantially improved health outcomes for patients with acute coronary syndrome. Both age-related physiological changes and accumulated cardiovascular risk factors increase the susceptibility to acute coronary syndrome over a lifetime. Compared with younger patients, outcomes for acute coronary syndrome in the large and growing demographic of older adults are relatively worse. Increased atherosclerotic plaque burden and complexity of anatomic disease, compounded by age-related cardiovascular and noncardiovascular comorbid conditions, contribute to the worse prognosis observed in older individuals. Geriatric syndromes, including frailty, multimorbidity, impaired cognitive and physical function, polypharmacy, and other complexities of care, can undermine the therapeutic efficacy of guidelines-based treatments and the resiliency of older adults to survive and recover, as well. In this American Heart Association scientific statement, we (1) review age-related physiological changes that predispose to acute coronary syndrome and management complexity; (2) describe the influence of commonly encountered geriatric syndromes on cardiovascular disease outcomes; and (3) recommend age-appropriate and guideline-concordant revascularization and acute coronary syndrome management strategies, including transitions of care, the use of cardiac rehabilitation, palliative care services, and holistic approaches. The primacy of individualized risk assessment and patient-centered care decision-making is highlighted throughout.